Awaken: Ultimate Shinobi
by Lord Atreyu Emyrs
Summary: After being kicked out of the orphanage again, Naruto stumbles upon something that could make him a God among men. Watch as he takes the world by storm and destroys all who seek to use him or those close to him! No pairings planned, Smart/Strong Naruto.
1. Chapter 1

Ultimate Shinobi

By: Lord Atreyu Emyrs

Chapter 1

It was a rainy 10th of October night, as young Uzumaki Naruto was walking through the alleys of Konoha. He had just been evicted from the orphanage for "destruction of property".

"As if I really broke a door down, I mean I'm only 5. Give me a freaking break", though Naruto as he trudged along with his meager belongings. He wore a simple pair of black pants with an orange shirt and a pair of blue sandals. On his back he carried a black back-pack with a few changes of clothes as well as some food and money that he had managed to "liberate" from the orphanage. "Serves them right." He thought defiantly. "Where am I going to go now", he said out loud. "Old-Man Hokage will just try to send me back to another orphanage." This wasn't the first time that Naruto had been kicked out, and each time the Hokage had sent him to a different orphanage to stay.

As he kept walking, while not really paying attention to where he was going, he was getting closer to parts of the village that was rarely traveled by civilians. Coming out of his thoughts, he looked up to see a sign that said "Keep Out: Forest of Death". Being the young child that he was the first thing that came to mind was…. "COOOOOLLLLL!".

Walking around looking for an entrance, he noticed the only way that he could get in was if he climbed the fence. "Ah man, was does everything have to be so hard," Said the frustrated young blonde. Making sure his back-pack was secure; he began to climb the fence. While climbing, the young boy's mind began to think about his life thus far. "Why is it that everyone either hates me or ignores me? I stay out of the way, I don't talk to anyone but Old-Man Hokage. So why pick on me?" You see, in the five short years of young Naruto's life, he had been mistreat more than some of the Maximum Security prisoners. He was rarely fed, always locked away by himself. He was only allowed out of his room when the Hokage came by to see him. Although he was rarely beaten, the villagers treatment of him made it so that he only cared for himself and a few others. Those few were the Hokage, an ANBU with a weasel mask, and another orphan named Tenchi. He hadn't seen Tenchi in months because he got adopted and his new family never let him visit the orphanage.

Once Naruto was on the other side of the fence he began walking again. After what seemed like years of walking to his young mind, which was only a few hours, he found a building covered almost completely by vines and weeds. "I wonder what's in there, don't look like anyone has been in there in forever", said Naruto to himself. Looking around for something to help remove the vegetation, he stumbles upon a jagged piece of metal. Attempting to pick it up he realizes that it is partially buried. "Why does Kami hate me so?" Using his bare hands, he starts to dig around the metal piece to try and free it. When he had dug deep enough, he pulled the debris from the ground. It was about one and a half foot long, extremely sharp on one end and cylindrical on the other. Staring in the hole he made he saw a same metal box that he decide to take with him. "Never know when it might be useful."

He took the metal piece, which he decided to call "Mr. Sharpy", over to what looked like it might be the entrance to the building. He worked tirelessly at the vines and weeds until he came to what looked to be a lock. Unfortunately it was unlike any lock he had ever seen. "All that work and it was for nothing, if I ever meet Kami I'm going to kick him or her in the butt," said an angry Naruto. Having nothing better to do he sat in front of the doorway and decided to look in the metal box he found. Retrieving it from his backpack he saw that it was roughly one foot by eight inches wide and about four or five inches deep. The top was inscribed with symbols that he couldn't read, the front contained a sophisticated lock that was, fortunately for him, unlocked. "Jeez, why put a lock on something if you not gonna use it. Oh well, works out for me…he he." Upon opening the box he found several ID sized cards as well as a few keys, and a round disc that was reflective on one side. "What the heck is this crap", thought Naruto. "Hey wait a minute, this key looks kinda like that lock." Jumping up quickly he ran to the door and tried the key. With an ominous groan and thick billowing smoke, the door slowly opened.

Gathering up his belonging, Naruto ran into the building, glad to have found a place to stay for at least one night.

**Unknown Location**

Deep underground several machines began awakening themselves. Power began flowing through cables and conduits that had remained dormant for centuries. In a darkened corner a ghostly figure came into view. "Intruder detected; Begin system start-up; Activate self-defense system; Prepare to repel intruder!"

**Normal P.O.V**

As soon as Naruto was fully in the building the door shut loudly behind him. "Oh boy, that's not good," he thought. Continuing onward he came upon a small pedestal with a large screen above it. On the pedestal were several slots, about the size of ID cards, a larger slot about the size of a CD, and a pad a little larger than an adult's hand.

Stepping to the pedestal Naruto wondered out loud, "Now what the heck is this thing?" Immediately after saying that he heard a voice speaking in a language he didn't understand. After several seconds he heard the same voice say, "Awaiting command codes for ending lock down procedure."

"Waiting for who to do what now", stated a confused Naruto.

"Six hundred seconds till self-destruct systems activate."

While Naruto may not understand a lot of things, he understood self-destruct pretty well. Panicking he moved closer to the pedestal and saw the slots, thinking quickly he opened the metal box again and took out the items. Placing the disc in its slot, he then moved on to the ID cards.

"Oh crap, which one goes in which hole?" Looking at the cards carefully he noticed a small number one in the top right hand corner hidden by a picture, and a number two and three on the other two. Reacting quickly he placed the cards in their corresponding slots and watched as two small doors opened on the pedestal. Looking at the screen he noticed it now said "Three hundred seconds till self-destruct systems activate".

"Danggit I'm wasting too much time." Said Naruto. Looking at the new slots on the pedestal, he realized that the holes were small and key shaped. Realizing this he looked at his three keys and immediately knew he had a problem. Looking at his keys again he realized that one was gold, one was silver, and one was bronze. He then looked over the key hole again and saw small slivers in each hole, one was bronze and the other was silver. Placing the keys in their appropriate slot, he waited for the countdown to stop. Looking at the screen he saw it continuing, he pressed and poke on the pedestal until finally he turned the keys. After turning the keys, the small pad lit up. Placing his hand there, the pedestal beeped and whistled, then he heard a loud klaxon. Looking at the screen he noticed it said "Thirty seconds till self-destruct systems activate", the countdown continued up till it reached three seconds when the klaxons stopped, and the screen went blanked. During all this all Naruto could think was "OH GOD, OH GOD, I'M GONNA DIE. I'M GONNA FREAKING DAY. KAMI, YOU TEME, I HATE YOU SO MUCH RIGHT NOW!"

When the screen lit up again it asked for a USER NAME, immediately on the pedestal a holographic keyboard appeared. Now while Naruto couldn't read very well, he still understood the alphabet, so he typed his name….. NARUTO UZUMAKI. After this happened, directly on the front of the pedestal, an ID card was printed with his face and name on it. He took it and looked at it oddly before he heard a noise behind him. Turning around he saw a ghostly figure walking through a door that he hadn't seen before.

"Who…what, are you?" Stuttered a scared Naruto, thinking it was a ghost.

The ghostly figure walked up to him and said, "Welcome, Master Uzumaki. How may I be of service to you.


	2. Chapter 2

Awaken: Ultimate Shinobi

By: Lord Atreyu Emyrs

Disclaimer: I do not own the Naruto series.

A/N: I tried to be as original as possible, but due to the fact that I have read a LOT of stories on this site, there is a possibility that I may unintentional copy some ones work. If that is the case I apologize now and ask that you let me know so that you may be credited for your ideas.

Chapter 2

"Ahhhhhhhhhhh, please don't kill, I'm sorry, don't kill me", were the first words out of Naruto's mouth when he heard the "ghost" finish speaking. He was beyond afraid, he had heard stories of how spirits would come and take people soul to Hell. Unknown to him, these stories were always said in his presence to frighten him, not because they were true.

"Why would I kill you Master Uzumaki?" was the response giving by the apparition. Upon hearing this Naruto stopped screaming and looked cautiously at the figure. He said, "Aren't you a ghost-y, come to take me to Hell?"

Her response was, "I am not a ghost. My name is EVE and I am the AI for this facility. Upon my awakening I am to report to the EIC, as you are the only living person with access to this laboratory the system lists you as the Boss." After explaining herself to her new master, she waited for instructions.

Naruto, while smart for his age, had no clue what half the things EVE said meant. But he sure did understand one thing, HE WAS THE BOSS! He didn't know what he was the boss of, but that didn't matter to him. He had something that was his and he wasn't about to let it be taken away.

"So, ummm, EVE right? What the Heck is an AI, or an EIC?" asked Naruto.

"AI means "Artificial Intelligence", it is basically a computer/computer program that is capable of thinking for itself. As for an EIC, that is the "Employee-In-Charge", Stated EVE.

"But I don't work here, I don't even know what HERE is", remarked a thoroughly confused blonde.

Naruto was more confused now than he had ever been. Here was this ghost-y, umm AI, telling him that he was in charge of some place that looked like it hadn't seen the light of day in YEARS, not only that but he was supposed to work there. "I must be dreaming, that's right, maybe it's from something I ate", he thought aloud.

"You are not dreaming Master Uzumaki, if you would follow me I will explain what is going on." Was the response to his musing by EVE.

Having nothing better to do, Naruto gathered his belongings and followed EVE through the partially hidden door. Going down several hallways they came upon a semi-reflective door, after a few seconds standing there the doors opened to show a small room that could hold maybe 10 people if they stood very close together. "This is an elevator, it is used to transport cargo to places quickly. This one only goes up and down; there are some here that go left and right as well. This will take us down to the actually facility, once there I will begin explaining."

He stepped into the elevator and began his descent. After several minutes the elevator stopped with a "DING" then the doors opened. Exiting the elevator he looked around this new area, it was fairly large about fifteen feet tall, fifty feet wide, and twenty five feet long. It was completely metal with several dark glass "windows" all around the room. Directly in front of the elevator was a larger desk with items on it he had never seen before.

After his quick visual inspection of the room EVE spoke up, "This is the main entrance for the facility; everyone must come in through this way to get in. Normally there would be several guards here to ensure nothing goes wrong. The monitors on the wall show the area we just came from, that is the only are visitors are allowed in, only employees may come down here."

EVE then took Naruto on a tour of the facility, and explained what was done there. She told him of how the scientists were doing research on ways to "improve" the human body, to make them faster, stronger, smarter, and more deadly. They searched for anyway they could to improve humans, until one day they thought they had found it. "It" was a type of virus that was capable of "reprogramming" certain parts of the brain that told the body how to function. They tested the virus on five individuals, only two of which survived. One became stronger, faster, and harder to damage. The other, he became a monster. The scientists belatedly realized that the virus itself had to be "programmed", you had to tell it what you wanted done and how. By just letting in choose at random there was no telling what you would get.

The individual who became a monster went on a rampage, destroying any and everything he came across. The other individual attempted to stop him but he was unsuccessful. Eventually the monster destroyed all life in the facility before it died from cellular degradation. The virus, let unchecked, continued to try and mutate him until he became nothing more than a puddle of ooze.

After the "Incident" the facility was forgotten, seeing as everyone who knew about it lived and worked in it. Without any human operators, EVE was left in charged and she continued the research as best she could. As she was unable to really work on the virus she set her attention to the technological aspect, creating weapons and items of great power. After a time when she had done all she was able to do with what little resources at hand, EVE set the facility in "Sleep" mode and remained that way until this day.

In the office of the Director, all Uzumaki Naruto could do was stand and blink, "So, what you're saying is that I have all that stuff and I can do whatever I want with it?"

"Yes Master Uzumaki. This facility is yours to do with as you see fit", replied EVE.

"I am so gonna kick ass when I learn to use this stuff", said the hyper active young demon container. "So, what do I do first?"

"In regards to what, Young Master?" queried a confused AI.

"Well I wanna be the best, well warrior I guess, don't really think those guys were ninja, huh?" said Naruto.

Searching her databanks for references on ninjas, EVE came to a startling discovery. Even though the facility was in "sleep mode" it still watched the area around it. She saw what the locals referred to as ninja and cross referenced it with what was know about ninja from her time. She was amazed; the ninja of now could have easily destroyed the monster that ravaged the facility. She concluded that if someone like them were give the virus they would become something akin to mythological gods.

Returning her attention to Naruto she replied, "No they were not ninja, but they were just as powerful. It seems that human have become powerful even with help. If someone with the abilities of a ninja were to use the virus, they could became one of the most powerful people alive."

"Coooool, so where do we begin", stated Naruto with a devious smirk marring his face.

"Watch world, Uzumaki Naruto is coming for round two and this time I ain't taking no prisoners."

A/N: I know the chapters are short, but I'm trying to get into the swing of things. Let me know what you guys think.


	3. Chapter 3

Awaken: Ultimate Shinobi

By: Lord Atreyu Emyrs

Disclaimer: I do not own the Naruto series, or anything else you may recognize.

A/N: There may be elements from either TV. shows or books, I don't own those either just taking a few ideas for a walk.

Chapter 3

Looking around the room, Naruto could only stare in awe and confusion at what he was seeing. The room was a large circle, with glass door cabinets containing liquids all colors of the rainbow. There were cables running to and fro, with what looked to be metallic arms connected to them. There was a large, stand up table, coffin looking thingy, he had no idea what it was but he just hoped he didn't have to go anywhere near it.

"If you would step over this way for a moment, we can begin your transformation," stated EVE, gesturing Naruto over to a row of odd looking TV's.

"Huh, what are looking at?" asked a confused blonde.

Replying to her master, EVE said, "This is a computer; it is one of many that control the machines in this room. By inputting commands you can tell the machines what you want done and how you would like it done. With this particular machine we are able to program the virus, whose name is Ultimus, to enhance your body to levels beyond what you could reach on your own."

Moving over to a cabinet with several needles in it, EVE retrieved one and turned toward the Kyuubi container, "If you would roll up one of your sleeves, I will retrieve a blood sample to test for any possible genetic mutations."

"Whaa…how did you pick up that needle, no wait…what do you think you are about to do with that BIG ASS needle. I ain't got no genny mutetas, or whatever you talking bout. So you can just go ahead and skip to the next part," flew from a distressed boy's mouth.

He and needles had never been good friends, nor had he and doctors for that matter. Walking backward ever so slowing, the young Uzumaki decided it was time to revert to drastic measures, meaning running very, very fast; very, very far away. Before he could take more than one step, one of the metallic arms came to life and lifted him from the floor, all while he was screaming and still trying to run. EVE patiently waited until he calmed down, twenty-three minutes later.

Calmly she answered his question, "I am a hard-light hologram, though I am not flesh and blood, nor metallic alloys; I am still able to interact with world if I so wish. The light I am made from is compacted and reflected in such a way that I am "solid". With the blood sample I am about to take I will be able to check for any mutations, or bloodline abilities as your people call them. Not only that, but there could be beneficial information written within your genetic code that could be used in the transformation."

"Huh?" was all he said.

EVE replied, "I will be testing to see if you have anything special in you."

"Well why didn't you say that? Do you gotta use all them big words and stuff?" replied a less confused Naruto.

Ignoring his question for the moment, EVE moved forward and drew blood before he was able to protest any farther. Directing the arm to release him, she beckoned him to follow her back over to the computers.

"Psycho ghost-y and her big needles, that hurt!" mumbled Naruto.

Once at the terminal, EVE placed the container of blood in a slot on the machine. After several seconds of odd noises, there was a beep and the monitor showed information that was all "English" to Naruto.

"So, what does that mean EVE", asked Naruto.

"This is basically the "instructions" for your body. With this I can find out about ANYTHING concerning your body. We could change it so that your hair is a different color; your eyes are a different color. Whatever you wanted different, this is the key."

"Cooooooool, so are you gonna make me, like a giant," asked the blonde.

"If that is what you wish to be, but you must remember that being a giant would make it hard for you to fit in with everyone else," replied EVE.

"OK, I guess," stated a bummed Naruto. "So what can we do then?"

EVE replied, "According to your wish to be the greatest warrior ever, we would first have to pick WHAT you wish to be able to do. There are multiple samples within this complex of beings whose genetic make-up could prove invaluable to you. Most of these beings are either from another planet or another dimension."

"I have no idea what you just said," was the response from a, yet again, confused blonde.

"Very well, just know that there is plenty here to help you in your goal," stated EVE.

"I suggest we first add the genetic code from a being we code-named "The Juggernaut", it is very strong while also be hard to hurt, its biggest weakness is psionic attacks. Psionic attacks are those which are caused by mental energy, such as telepathy (the ability to talk mind to mind or attack the mind directly), telekinesis (the ability to move things with the mind), pyrokinesis (the ability to create and/or control fire with the mind), psionic bolt (the ability to use condensed mental energy to fire bolt that affect the physical world), and astral projection (the ability to create a ghost like version of yourself to explore an area). Seeing as Juggernaut is vulnerable to psionic attacks, the next genetic code added to you would be from Psion. The last genetic code will be added from a very unique being, it has the ability to manipulate energy to its will. It doesn't matter what the energy type is, so long as there is a source of energy nearby it can use it. This being was code-named "Sorcerer", because many thought its power was magical in nature."

"WOW, they sound so cool. But wait I only get three gennicode thingies? How is that gonna make me the most powerful warrior ever," asked Naruto.

"With just those three genetic codes, as well as the standard overall upgrade from Ultimus, that is all you need. You will be THE strongest person alive physically because of Juggernaut, with the power of a Psion you'll have no problems matching, and beating, anyone mentally. Add to that the ability to use ANY type of energy that exists anywhere and you've just became a Kami among Men," replied EVE.

"So how do we start," asked an excited Naruto.

"Now," said EVE. Entering several commands into the computer, EVE waited while the specifically designed Ultimus for one Naruto Uzumaki was created. After several minutes EVE moved toward a table with several straps beckoning for Naruto to follow her. After checking the table and the cable and wires connected to it, she turned toward Naruto.

"If you will climb up here and lay down we can begin the procedure."

"Umm, is this going to hurt, and why are there straps on the table?" asked a confused Naruto.

"It may hurt, I do not know. The straps are to keep you in one stop until we are done so that there will be no errors in the procedure."

Gathering up his courage, Naruto jumped up on the table and lay down. Once he was comfortable the straps snapped into place preventing him from moving.

"You know I really don't think this was a good idea," thought the blonde.

"Right now I'm connecting the monitors and an I.V. to you so I can watch your health as well as provide your body with nutrients. The procedure is very hard on the body because it uses up all of the body's stored energy," stated the A.I.

Done with her explanation, EVE moved to the head of the table and began the process. As soon as the virus entered Naruto's body all he knew was pain. It felt as if every part of him was being dipped in acid while being fried and frozen all at the same time. After what felt like eternity to him, he passed out.

*MINDSCAPE*

Opening his eyes, Naruto saw that he seemed to be in an old abandoned, and flooded, building. "Well ain't this just nice, I knew I had to be dreaming. Ain't no way nothing good like that would happen to me." Looking around Naruto saw that he had only one way to go so decided to follow it and see where it led. After walking for what seemed like hours, he came to the largest room he had ever seen in his life. As far as he could tell it had no side or back walls, only the wall that held the door which he came through and it seemed to go on forever.

"What the…what the heck is in here," stated Naruto. Before he had finished his sentence good he heard a loud, pain-filled roar.

"**YOU WORTHLESS HAIRLESS BABOON, IF THIS SEAL WASN'T HERE I'D GRIND YOU INTO MEAT PASTE! TO THINK, THE GREAT KYUUBI WAS DONE IN BY A PRE-PUBESCENT MINI-APE, WHEN I'VE SHAT BIGGER THAN YOU!"**

"Where the heck am I and who the heck are you, and don't gimme that Kyuubi crap, everybody knows the 4th killed it," said a scared and confused blonde.

"**FOOL, YOU THINK A MERE HUMAN COULD DESTROY A BEING LIKE ME. HAHAHAH, SUCH FOOLISH THINKING. I AM KYUUBI, THE GREATEST OF THE TAILED-BEASTS. WHEN I CAME TO THIS KAMI FORSAKEN VILLAGE I WAS ATTACKED AND SEALED AWAY INTO YOU. AS TO WHERE WE ARE, WE ARE IN YOUR MIND. NONE OF THAT MATTERS NOW, BECAUSE OF YOU I'M DYING. I JUST WISH I COULD TAKE YOU WITH ME. WHATEVER YOU HAD PUT IN YOU IS DESTROYING ME AND ABSORBING MY POWER."**

"So you are the reason that the villagers hate me, hah, I'm glad you're dying. You caused me all this pain, but at least I get something out of it…..YOUR POWER!," yelled Naruto.

With that proclamation, the Ultimus "virus" rushed in and began assimilating the Kyuubi. While the Kyuubi no longer had a body, it was still a very powerful being. Composed entirely of mental energy, spiritual energy, and mana (magic) it was one of the most powerful earth-bound entities Naruto would every come across. But because of the Kyuubi the Ultimus "virus" now had a problem; it would still be able to do its standard upgrade, which was increased strength, speed, regeneration, improved hearing, eyesight, and toughness. It would also be able to add the Juggernaut code, as well as the Psion code. The problem was adding the Sorcerer code and what to do with the genetic coding it obtained from the Kyuubi, which confused it greatly as the Kyuubi had no body so it should have no genes yet it still obtained them from the mass of energy. Not knowing how to solve this dilemma it decided to place the choice within its host's hand. Morphing into a humanoid form, it presented the problem to its host.

"We have destroyed the one known as Kyuubi. We are now unsure as to how to proceed with the procedure."

"Who are you," asked a confused blonde. He seemed to be more confused in the pass day than in his whole life.

"We are Ultimus. We are unable to proceed due to the unforeseen presence of the Kyuubi. With its destruction, we now have new genetic coding and a mass of energy that we have no instructions for. How do you wish to proceed?

"Um, ok then. I guess you can just add the stuff from Kyuubi to me, but um...make sure I don't grow fox ears or a tail or anything cause that would be bad," replied a stunned blonde.

"As you wish." Returning to its work, Ultimus took the genetic code and added what parts it code to him without making him physically change. The first change was to his eyes, they were enhanced to the point where ninjas would think he had a bloodline, when actually they were just the normal eyes of Kyuubi. His eyes were now a weaker version of the Byakugan and the Sharingan. All that was missing was the x-ray vision of the Byakugan and the copying ability of the Sharingan. Next, Ultimus took the Kitsune's ability of shape-shifting and added it to the blonde. Lastly was an ability that no one but the Kyuubi knew it had, the ability to absorb other demons and take their raw power as its own. It could not absorb special abilities only their raw chakra, mana, or spiritual energy.

Once done with the genetic coding of the Kyuubi, Ultimus then merged the energy it had take from the demon into its host's chakra coils. This caused Naruto's body to go through a fundamental change, no human body is meant to handle that amount of power so the power changed the body to something that could handle it. As he already had the genetic coding of a demon within him, the mass of energy decided to finish the process. Not having any specific demon to use, it found the nearest animal to make the change.

Not far from the room that Naruto was in, was a room with several specimen in suspended animation. A tendril of power seeped out and searched from something it could use. Upon reaching the room the first being it came across was unfortunately not an animal, but it was running out of time so it had to use what it could. Absorbing the body of the specimen the tendril of power retreated back into the blonde and finished the transformation.

While the energy mass was finishing its procedure, Ultimus put the finishing touches on its host. Making sure that all previous changes took hold, it added the last, which was the genetic coding of the Sorcerer. Once the Sorcerer code was entered, the normal procedure for the Ultimus "virus" was to destroy itself as its work was done. This particular "virus" had been changed due to coming in contact with the Kyuubi, so not knowing what to do it contacted its host once again.

"The procedure has been completed, awaiting further orders."

"Um, ok. What else is there to do….better yet what else can you do?" asked Naruto.

"We have completed our orders; any further changes must be made by you. All that we contain now is the knowledge of the Kyuubi.

"OK, so could like, I don't know merge with my brain or something," asked the former demon container. Unknowingly, the mistake that he had just made would prove to be one of his greatest assets one day, if he survived. Instead of asking for the knowledge from the Kyuubi, he had mistakenly asked the Ultimus "virus" itself to bond with him, permanently.

"Orders received." The Ultimus "virus" began spreading throughout his mindscape and embedding itself into the walls. Once it began all Naruto knew was darkness.

*REAL WORLD*

Eve looked up at the monitors as they all showed that Naruto's heart had stopped beating and he was no longer breathing.

A/N: The chapter didn't quite "flow" the way I wanted it too, but I can't seem to figure out where I screwed it up at, lol. Let me know what you think, thanx!


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